Hi Dr Greve, Thank you very much for the great answers.

Kindly, I have one last question.

The range of the signal intensity within the voxels in the original SUV maps is min=0.00 and max=3.017629

For the mgx images it is min=-43.74384 and max=88.468712

The difference in the range of signal intensity in the mgx images is largely wide. It seems that PVC increases the signal intensity. Is this correct?

Am I doing something wrong. I plan to include these images in voxel-wise analysis so I am curious about this difference between the images.

Thanks for any clarification!

On 8/18/17 10:20 AM, John Anderson wrote:

Hi Dr Greve,

I followed the steps in WIKI to do SUV-surface based analyses + PVC. I have the following questions and I highly appreciate your input:

1. Why the dimension of the images (mgx.gm, mgx.ctx.gm and mgx.ctx.subgm) is not like the original SUV image that has been fed to the pipeline. i.e. I start with image-dimensions 128X128X128 : 2X2X2 and end up with 79X113X102 : 2X2X2

Also FOV is different as well between the original SUV image /256/ and the output mgx images /158/. How this happen? I am I doing something wrong?

I set up mri_gtmpvc to reduce the field of view to a bounding box around the head to reduce memory and computational loads. You can turn this off with --no-reduce-fov

2. Some voxels in the mgx images has negative signal intensity. is this normal?

Yes. MG works by estimating the contribution of non-GM to GM and subtracting it out. If the estimate is too high, then it can cause negative values.

Thank you for any clarification.

John